The naval officer in charge of an asylum seeker boat shortly before it exploded killing five Afghan men has broken down while giving evidence at a coronial inquest into the deaths.

The inquest, being held in Darwin, has heard evidence the fire on the SIEV 36 was deliberately lit with matches or a cigarette lighter.

Chief Petty Officer Faunt told the inquest if he had been in charge of the naval party that first boarded the boat he would have confiscated lighters and matches, whether or not there was petrol on board.

Later, when he was on board the boat, he did not have enough manpower to take the items from the passengers.

But he said in hindsight he should have removed matches from the boat's cabin.

Chief Petty Officer Faunt has suffered post traumatic stress disorder since the fatal blast in April last year.

He was overcome with emotion when asked how much sleep he had had in the time leading up to the explosion, leading to the inquest being briefly adjourned.

The inquest has previously heard Navy personnel were rescued from the water before the boat's passengers, in line with naval procedure.

But Chief Faunt said his training did not require Australian Defence Force members to be rescued first.

He said Navy personnel did not stand back and were active in rescuing the boat's passengers.